The Okavango Delta and Kwando /Lenyanti /Chobe River system (herein referred to as the "Lynyanti") are the country's major perennial water sources. The work reported here has shown that the natural variation results, as anticipated, in considerable uncertainty in interpretation of environmental data. These findings are particularly important because they demonstrate that water quality indicator variables cannot be based on average values. Since rainfall varies greatly from year to year, import of salts and suspended sediments into the delta is also highly variable. This suggests, therefore, that future water quality models should be based on a probabilistic rather than deterministic approach.